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Vertical Distribution Patterns of Plankton and Their Relationship to Physical Factors Over the Continental Shelf Off Oregon

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Vertical Distribution Patterns of Plankton and Their Relationship to Physical Factors Over the Continental Shelf Off Oregon AN ABSTRACT OF THE DISSERTATION OF Malinda Sutor for the degree of Doctor of Philosophy in Oceanography presented on June 4, 2004 Title:Vertical Distribution Patterns of Plankton and Their Relationship to Physical Factors over the Oregon Continental Shelf Abstract approved: Redacted for privacy T mot1T J. Cowles Discrete layers of phytoplankton and zooplankton were observed over the Oregon continental shelf in summer and fall of 2001 and summer 2002 using optical and acoustical technologies and a pump sampling system. Layers of phytoplankton had steep vertical gradients which were associated with gradients in density and local peaks in shear. These layers had high concentrations of chlorophyll andwere persistent for hours to days. The optical signature of co-occurring shallow and deep layers indicated that these layers may have differentsources and temporal evolution patterns. Layers of zooplankton were often collocated with layers of phytoplankton. Optical indicators of in- situ grazing were not correlated to zooplankton biomass, indicating that collocated layers containing high abundances of phytoplankton and zooplanktonmay not be areas of maximal grazing. Acoustic backscatter resolved distributionpatterns of zooplankton that were not resolved with stratified net systems or direct pump samples. The size and orientation of zooplankton had large affectson acoustic backscatter and the magnitude of acoustic backscatter was not always correlated to zooplankton biomass. ©Copyright by Malinda Sutor June 4, 2004 All Rights Reserved Vertical Distribution Patterns of Plankton and Their Relationship to Physical Factors over the continental shelf off Oregon By Malinda Sutor A DISSERTATION submitted to Oregon State University In partial fulfillment of the requirements for the degree of Doctor of Philosophy Presented June 4, 2004 Commencement June 2005 Doctor of Philosophy dissertation of Malinda Sutor presented on June 4, 2004 APPROVED: Redacted for privacy Major Professor, representing Oceanograph Redacted for privacy Dean of the College of Oceanic and Atmospheric Sciences Redacted for privacy Dean of the Graduate School I understand that my dissertation will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release ofmy dissertation to any reader upon request. Redacted for privacy Malinda Sutor, Author ACKNOWLEDGMENTS I would like to acknowledge themany people who helped with the collection and processing of the data used in this dissertation, provided helpful commentson the text, and provided important insight to the results. My major professor, TimCowles, has been a wonderful mentor and has tirelessly provided important guidance and insight to this work as well as continual encouragement. Committee members Charlie Miller and Bill Peterson have been dedicated editors and have been important scientificmentors. Committee member Duncan McGehee provided guidanceon acoustic methods. Committee member Mike Kosro provided important data and guidancein the interpretation of that data. Others who have provided importantassistance are: Mark Benfield, Krista Longnecker, Jamie Gomez-Guttierez,Jesse Lamb, Russ Desiderio, Cidney Howard, Lisa Eisner, Julie Kiester, Patrick Ressler,Anders Roestad, Gareth Lawson, Joe Warren, Lew Incze, Bob Campbell, Peter Wiebe,Van Holliday, Charles Greenlaw, Hal Batcheldor, and all the members of TimCowles' lab group. I would also like to acknowledge Dudley Chelton and MikeFrielich for their instruction and help in the data analysis courses which laid the foundationfor much of the data analysis in this dissertation. CONTRIBUTION OF AUTHORS Tim Cowles, Bill Peterson, and Steve Pierce provided data used in Chapter 1 and provided comments on the analysis and presentation of that data. Bill Peterson and Jesse Lamb provided data and assisted in analysis of data for Chapter 3. Juanita Urban-Rich and Mike Kosro provided data and Tim Cowles providedcomments on the analysis and presentation of data in Chapter 4. Mike Kosro provided data and Tim Cowles provided comments on the analysis and presentation of data in Chapter 5. TABLE OF CONTENTS Page 1 Introduction 1 1.1 References 9 2 Acoustic Observations of Finescale Zooplankton Distributions in the Oregon Upwelling Region 12 2.1 Abstract 12 2.2 Introduction i 2.3 Methods 16 2.4Results 19 2.5 Discussion 29 2.6 Conclusions 38 2.7 Acknowledgments 38 2.8 References 39 3 Effect of Orientation of Euphausiids and Copepodson Acoustic Target Strength: Implications for Measurements from Down-looking and Side-lookingAcoustic Systems 44 3.1 Abstract 44 3.2 Introduction 45 3.3Methods 47 3.3.1Individual Target Strength 48 3.3.2 Predicted Volume Backscatter 51 3.4Results 55 3.4.1Individual Target Strength 55 3.4.2 Predicted Volume Backscatter 64 3.5 Discussion 69 3.6 Conclusions 72 3.7Acknowledgements 73 3.8 References 74 4 Comparison of Acoustic and Net Sampling Systemsto Determine Patterns of Zooplankton Biomass and Taxonomic Groups 77 4.1 Abstract 77 4.2 introduction 78 4.3 Methods 85 4.3.1Collection and Analysis of Acoustic and Net Data 85 4.3.2 Calculations of Predicted Backscatter 92 4.3.3Inverse calculations 92 4.4Results 93 4.4.1 Comparison of Measured Sv from TAPS andHTI 93 4.4.2 Comparison of MeasuredSv and Biomass from MOCNESS 109 TABLE OF CONTENTS (Continued) Page 4.4.3 Comparison of Predicted and Measured Sv 112 4.4.4 Analysis of SNR and Numbers of Individuals in Ensonified volume 124 4.4.5 Comparison of Inverse Results and MOCNESS data 126 4.5 Discussion 129 4.5.1Comparison of Measured Acoustic Data and Biomass Patterns 129 4.5.2 Comparison of Predicted and Measured Sv 131 4.5.3 Comparison of Inverse Results and MOCNESS Data 133 4.5.4 Comparison with Past Studies 136 4.6 Conclusions 137 4.7 Acknowledgements 139 4.8 References 140 5 Observations of Finescale Vertical Plankton Distributions and Associated Physical Parameters i 42 5.1 Abstract 142 5.2Introduction 143 5.3 Methods 147 5.3.1Study Site 147 5.3.2 Instrumentation 149 5.3.3 Data and Sample Collection 152 5.3.4 Sample Analysis 154 5.3.5 Data Analysis 155 5.4 Results 158 5.4.1Vertical pattern of Chlorophyll and its Relationship with Vertical Shear and Density 158 5.4.2 Relationship between Volume Backscatter and Chlorophyll Peaks 164 5.4.3Vertical Patterns in Biomass and Taxonomic Composition 165 5.4.4 CDOM 171 5.5Discussion 174 5.5.1Distributional Patterns of Phytoplankton and Zooplankton 174 5.5.2 Consequences of Coarse Scale Sampling 177 5.5.3 Vertical Grazing Patterns 181 5.5.4 Summary 184 5.6 Conclusions 185 5.7 Acknowledgements i 86 5.8 References 187 6 Characteristics and Mechanisms of Formation and Maintenance of Phytoplankton and Zooplankton Layers Observed in Summer and Fallover the Oregon Continental Shelf and Their Potential Ecological Roles 191 6.1 Abstract 191 TABLE OF CONTENTS (Continued) Page 6.2 Introduction 192 6.3 Methods 195 6.3.1Data and Sample Collection 195 6.3.2 Data and Sample Analysis 196 6.4Results 198 6.4.1Character of Phytoplankton Layers 198 6.4.2 Character of Backscatter Layers 201 6.4.3 Relationship between Gradients in Phytoplankton, Buoyancy Frequency, and Vertical Shear 201 6.4.4 Relationship between Chlorophyll, Phytoplankton, and Microzooplankton Distributions 207 6.4.5 Relationship between Chlorophyll, Acoustic Backscatter, and Mesozooplankton Distributions 210 6.4.6Contrasting Characteristics of Shallow and Deep Phytoplankton and Zooplankton Layers 214 6.5Discussion 222 6.5.1Character of Phytoplankton Layers 222 6.5.2 Relationship between Gradients in Phytoplankton, BuoyancyFrequency, and Horizontal Velocity 224 6.5.3Possible Mechanisms of Formation and Maintenance of Phytoplankton Layers 226 6.5.4 Relationship between Phytoplankton, Acoustic Backscatter,and Mesozooplankton Distributions 227 6.5.5 Contrasting Characteristics of Shallow and Deep Phytoplanktonand Zooplankton Layers 229 6.5.6 Possible Mechanisms of Formation of Shallow and DeepPhytoplankton Layers 231 6.5.7 Temporal Evolution of Deep Phytoplankton Layer 233 6.5.8 Possible Mechanisms of Formation of Shallow andDeep Mesozooplankton Layers 234 6.5.9 Potential Ecological Roles of Shallow and Deep PlanktonLayers 234 6.6 Conclusions 237 6.7 References 239 7 Conclusions 242 7.1 References 251 8 References 252 Appendices 264 TABLE OF CONTENTS (Continued) Page Appendix AInverse Acoustic Methods: Evaluation of Assumptions and Error and Comparison with Direct Samples 265 A. 1 Assumptions of Inverse Method 265 A.2Inversion Method 266 A.3Data Requirements 267 A.4Development of Inversion Method 271 A.4.l Collection and Analysis of Acoustic and Net Data 271 A.4.2 Inversion of Acoustic Data 271 A.5Evaluation of Scattering Models 276 A.6Evaluation of Data Used in Inversion 279 A.7Evaluation of Scattering Models 280 A.8Best Methodology 289 A.9References 290 Appendix BComparison of Pump, Niskin Bottle, and Vertical Net Samples 292 B. 1 Density and Taxonomic Composition of Niskin Bottle and Pump Samples 292 B.2Density and Taxonomic Composition of Net and Pump Samples 293 B.3Length Distribution Comparisons of Vertical Net and Pump 294 B.4Kolmogorov-Smirnov Goodness of Fit Test for Continuous Data 296 B.5References 297 LIST OF FIGURES Figure Page 2.1. Map of the study area off the coast of Oregon. 17 2.2. Wetstar fluorometer voltage with density() contours from CTD overlaid 20 2.3. Example profile of density (A), buoyancy frequency (N2) (B), and fluorescence (C) from Station 1.. 21 2.4. Volume backscatter (Sv) from 120 kHz 23 2.5. Average volume scattering spectra for layers 1A, 2A, and 3Aat the four frequencies 38, 120, 200, and 420 kHz 24 2.6. Horizontal velocity from shipboard 150 kHz ADCP 25 2.7. Northward velocity contours (m s') overlaidon 120 kHz Sv 28 2.8. Plot of theoretical target strengths at different frequenciesfor several different organisms (6 mm long copepod, 2mm diameter shelled pteropod, 2.5 cm long euphausiids). 32 3.1. Reference incident beam directions for individualtarget strength calculations in a sperical coordinate system 49 3.2.
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